Protein profile

KP13_00058

D-galactonate dehydratase

Genome: KpKP13

Gene: AHE41982.1 dgoD Structure source: AlphaFold + ColabFold UniProt A0A0H3H0G1

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Amino acids 382

Annotations 5

Features 29

PDB binders 7

Druggability 0.604

Overview

Basic information about this protein and its source genome.

Accession: KP13_00058
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE41982.1 dgoD
Status: annotated
Amino acids: 382
Structure source: AlphaFold + ColabFold

4.2.1.6

GO:0008869 Catalysis of the reaction: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O. GO:0034194 The chemical reactions and pathways resulting in the breakdown of D-galactonate, the anion of D-galactonic acid. GO:0009063 The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents. GO:0000287 Binding to a magnesium (Mg) ion.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 25.773
Human E-value: 4.31e-10
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 94.92

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.604

Structure A0A0H3H0G1

Pocket Pocket 1

P2Rank 0.936

Structure A0A0H3H0G1

Pocket Pocket 1

ColabFold model

FPocket 0.388 · Pocket 11

P2Rank 0.924 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 196 / 4744 genomes with a hit

Normalized 0.041

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

4.2.1.6

Gene Ontology (GO)

GO:0008869 Catalysis of the reaction: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O.
GO:0034194 The chemical reactions and pathways resulting in the breakdown of D-galactonate, the anion of D-galactonic acid.
GO:0009063 The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
GO:0000287 Binding to a magnesium (Mg) ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

29 records

Show feature table

Start	End	DB	Term	Name
107	342	FunFam	G3DSA:3.20.20.120:FF:000008	D-galactonate dehydratase
102	345	Gene3D	G3DSA:3.20.20.120	-
102	345	InterPro	IPR036849	Enolase-like, C-terminal domain superfamily
125	230	SMART	SM00922	MR_MLE_2
125	230	InterPro	IPR013342	Mandelate racemase/muconate lactonizing enzyme, C-terminal
15	107	Pfam	PF02746	Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
15	107	InterPro	IPR013341	Mandelate racemase/muconate lactonizing enzyme, N-terminal domain
139	355	Pfam	PF13378	Enolase C-terminal domain-like
139	355	InterPro	IPR029065	Enolase C-terminal domain-like
2	353	CDD	cd03325	D-galactonate_dehydratase
2	353	InterPro	IPR023592	D-galactonate dehydratase
180	211	ProSitePatterns	PS00909	Mandelate racemase / muconate lactonizing enzyme family signature 2.
180	211	InterPro	IPR018110	Mandelate racemase/muconate lactonizing enzyme, conserved site
1	369	SFLD	SFLDF00003	D-galactonate dehydratase
1	369	InterPro	IPR023592	D-galactonate dehydratase
1	362	PANTHER	PTHR48080	D-GALACTONATE DEHYDRATASE-RELATED
1	362	InterPro	IPR034593	D-galactonate dehydratase DgoD-like
95	357	SUPERFAMILY	SSF51604	Enolase C-terminal domain-like
95	357	InterPro	IPR036849	Enolase-like, C-terminal domain superfamily
14	357	Gene3D	G3DSA:3.30.390.10	-
14	357	InterPro	IPR029017	Enolase-like, N-terminal
1	112	SUPERFAMILY	SSF54826	Enolase N-terminal domain-like
1	112	InterPro	IPR029017	Enolase-like, N-terminal
82	107	ProSitePatterns	PS00908	Mandelate racemase / muconate lactonizing enzyme family signature 1.
82	107	InterPro	IPR018110	Mandelate racemase/muconate lactonizing enzyme, conserved site
1	116	FunFam	G3DSA:3.30.390.10:FF:000003	D-galactonate dehydratase
1	369	SFLD	SFLDS00001	Enolase
1	382	Hamap	MF_01289	D-galactonate dehydratase [dgoD].
1	382	InterPro	IPR023592	D-galactonate dehydratase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3H0G1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00058	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.604

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				23.49	0.889
2				1.58	0.024

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
11				0.388

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	24.18	0.896
2	2.26	0.056
3	1.99	0.043
4	1.3	0.014

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

57 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CS2	3P93	Q1QT89	196.2 Da LogP -3.49 TPSA 138.5	1 viol.	✓ Clean	`C([C@H]([C@H]([C@@H]([C@@H](C(=O)O)O)O)O)O)O`
EZ4	3RGT	Q1QT89	179.1 Da LogP -2.65 TPSA 127.4	✓ Ro5	✓ Clean	`C([C@H]([C@H]([C@@H](C(=O)N=O)O)O)O)O`
KDG	3P93	Q1QT89	178.1 Da LogP -2.26 TPSA 115.1	✓ Ro5	✓ Clean	`C([C@@H]([C@@H](CO)O)O)C(=O)C(=O)O`
LMR	4JN7	B9JNP7	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@@H](C(=O)O)O)C(=O)O`
MLT	3RR1	B2UCA8	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)C(=O)O`
NHE	3V3W	B3PDB1	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCS(=O)(=O)O`
TLA	3V4B	B3PDB1	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@@H]([C@H](C(=O)O)O)(C(=O)O)O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1710230	1.000	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC11592819	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC11592820	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)…`
ZINC11592821	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O…`
ZINC1531006	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O…`
ZINC1531007	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)…`
ZINC33991088	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H]…`
ZINC34049524	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)[C@@H](O…`
ZINC34370883	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](…`
ZINC4403706	0.950	256.2 Da LogP -4.77 TPSA 178.9	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H…`
ZINC4403707	0.950	256.2 Da LogP -4.77 TPSA 178.9	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H…`
ZINC4403708	0.950	256.2 Da LogP -4.77 TPSA 178.9	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H]…`
ZINC4403709	0.950	256.2 Da LogP -4.77 TPSA 178.9	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H]…`
ZINC4521295	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H…`
ZINC4521296	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H]…`
ZINC4521297	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H]…`
ZINC4521298	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](…`
ZINC5830322	0.950	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)…`
ZINC2004372	0.786	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.786	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC2562361	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC3870003	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC8551322	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC8551323	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC8551324	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC2562359	0.708	268.2 Da LogP -4.17 TPSA 175.7	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)[…`
ZINC71773889	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@H](O)C(=O)O`
ZINC71773890	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC71773891	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC12359024	0.632	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC13533920	0.632	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532740	0.632	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593	0.632	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC2013424	0.632	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021	0.632	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC3860635	0.632	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O`
ZINC5783661	0.632	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC6072527	0.632	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC100036265	0.625	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC100071552	0.625	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CO`
ZINC113074329	0.625	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC13522679	0.625	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC4353160	0.625	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)CO`
ZINC8579422	0.625	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC4726346	0.600	225.2 Da LogP -4.73 TPSA 164.5	1 viol.	✓ Clean	`NC(=O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H…`
ZINC4726347	0.600	225.2 Da LogP -4.73 TPSA 164.5	1 viol.	✓ Clean	`NC(=O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H]…`
ZINC4726348	0.600	225.2 Da LogP -4.73 TPSA 164.5	1 viol.	✓ Clean	`NC(=O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H]…`
ZINC4726349	0.600	225.2 Da LogP -4.73 TPSA 164.5	1 viol.	✓ Clean	`NC(=O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](…`
ZINC5372851	0.577	211.2 Da LogP -4.07 TPSA 150.5	1 viol.	✓ Clean	`O=C(NO)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)CO`
ZINC5372854	0.577	211.2 Da LogP -4.07 TPSA 150.5	1 viol.	✓ Clean	`O=C(NO)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.